Simulation and Analysis of Nucleic Acids

We will develop the Nucleic Acid Workbench, a commercial software program for use in the study of nchemistry. This software will address three broad areas: construction of nucleic acid systems, simulnucleic acids, and analysis and visualization of nucleic acid structures. Single, double and triplemodified nucleic acids in A, B, Z and parallel forms will be supported, including hybrid structureschain forms. A series of simulation studies using a number of commonly used forcefields will be perfstructures and energetics of nucleic acid systems. Differing charge models and solvation models willAnalysis tools will be provided to describe chain geometries and chain interaction geometries. A suibenchmarks will be generated and used to compare four commonly used forcefields, allowing users of nsimulation studies to more carefully calibrate and assess the results of these simulations. All eleminteractive graphical user interface and three dimensional visualization techniques. The Nucleic Acimarketed by Molecular Simulations, a company which develops and markets chemical simulation software